Operation Rising Phoenix
by Tyber Zahn
Summary: Another OC based one, but this time the focus is on a certain black hedgehog and a human... Has those two in flashbacks, starting in a later chapter.
1. A rude Awakening

Chapter one: Rude Awakenings

**Omega Corps Medical wing**

"Tyber, Tyber wake up already." Mary said as she sat next to Tyber's bed. "What did this to you?"

"How is he?"

Mary turned to see Robert, her husband and Tyber's father. "Not good, whatever hit him dealt a lot of damage."

Robert shook his head, "Tyber what happened?"

**Tyber's mind**

Psionics had the ability to sense ripples caused by intense emotion. So Tyber was used to seeing things, but not like this. When he saw something it was an imprint caused by emotion, not a vision, more like watching a history video. But he couldn't explain what he was seeing now. Mainly because he didn't know how far back in time he was seeing, or if he was having a vision of the future, and the fact that he was in a coma and not able to detect emotional ripples confused him to no end.

He was running down a large metal corridor, holding someone's hand. He wasn't sure who it was, but the person was significantly taller than him. He looked back and saw the person's face, it was the face of a young human girl, and she was blond, about ten or twelve years old. He had never met her, but she seemed familiar. She was wearing a light blue dress, but she seemed afraid of something. Both of them were panting, like they'd been running for either a long time, or they'd gone a long distance. A few minutes later she let go of her hand he looked back to see soldiers. G.U.N. soldiers, why was G.U.N. here? He saw her look back at him and hold her hand out, and then he heard the gunshot. He saw the girl fall, when she hit the ground he heard himself yell, "Maria!" He knew he was feeling the emotions of whoever's eye's he was seeing through, and he felt like he lost everyone he ever knew, everyone he'd ever loved. All of them gone, with just one gunshot. He didn't see who pulled the trigger, but he was going to make them pay.

**Omega Corps Medical wing**

Tyber opened his eyes slightly and groaned, "Ouch."

Mary rushed over to his bed and grabbed his hand, "Tyber can you hear me?"

Tyber nodded, "Yeah, I can hear you. Where am I?"

"You were picked up by a G.U.N. medical crew. Do you remember anything?"

Tyber shook his head, "No, all I know now is that my whole body is hurting.

Mary nodded and hit a button on his monitor, morphine pumped down through his IV and into his body.

Tyber sighed, "That's better. Thanks."

"You're welcome, so you don't remember anything?"

Tyber shrugged, "No, how long was I out?"

"About a month now, you were hit pretty hard."

"Wow, it only felt like a few minutes."

Mary cocked her head to the side, "That's odd, it normally only feels like a second. Did you see something while you were out?"

Tyber nodded, "Not sure what, but I saw something. I was in a base of some kind, it had metal hallways. I was with a girl, human, a few years younger than me. But the thing that scared me the most is that she was killed, by G.U.N. soldiers. We killed her. It just doesn't feel right."

Mary nodded, "When you feel better you should investigate it. Your instincts about things like that are rarely wrong."

"True," Tyber smiled, "I'll look into it."

**Omega Corps Archive: Two weeks later**

"This is getting me nowhere." Tyber said as he searched G.U.N. records on people named Maria. "Maybe I'm looking in the wrong place, maybe I'll be better off asking someone who has been here longer than me." He shook his head, "Who in the world should I ask? Shadow, no he'd more than likely deck me. Maybe I should ask the Commander? He owes me a favor anyway."

**G.U.N. Global Defense HQ: Next day**  
"Tyber, I didn't expect to see you so soon."

Tyber chuckled, "Same here Commander, but I want to call in that favor."

The Commander nodded, "Alright, what do you need?"

"Information, a bio to be precise. I need information on someone, I, saw."

The Commander nodded, "Who did you see?"

Tyber sighed, "Some girl named Maria, I don't know much about her. I don't even know where on earth, or if I was on earth, I am in the vision." Tyber stopped there; he didn't want the Commander to think he was crazy.

"I know Psionic sensitive beings can detect and relive experiences, by finding an Emotional Ripple right?"

Tyber nodded, "Yeah, how did you know that?"

The Commander shrugged, "When you're my age, you know a lot." He motioned for Tyber to continue.

Tyber closed his eyes, "She's ten to twelve years old, taller than me by a significant amount. She's blond, has blue eye's I think?" He shook his head, "She was wearing a blue dress. I was in what looked like a metal corridor, we were being chased, and then she got shot. By G.U.N. soldiers, I heard myself cry out, Maria!" He looked at the Commander and it looked like he was crying. "Commander, what's wrong?"

The Commander wiped a tear from his eye, "The girl you're seeing is named Maria R. she is the cousin of Dr. Eggman, and the granddaughter of Professor Gerald."

Tyber went pale, "You mean, **that **Maria? The one Shadow tried to avenge by blowing up the Earth?"

"Yes, she was a good friend to me, and to Shadow."

Tyber shook his head, "So what should I do?"

Commander chuckled, "You're the genius General, figure it out." Tyber could tell that the Commander knew what Tyber should do, but wanted him to figure it out for himself.

Tyber rubbed his chin, "I think it's about time I take a trip to the ARK."

**Me**: Thought that there wouldn't be an author's note? Wrong, how do you like it so far?


	2. The Sky is not the limit

Chapter two: The sky is NOT the limit

**AN:** Uh, this is considerably embarrassing. I posted this as chapter one, I corrected it, but I am sorry for those of you thought this was chapter one and were confused.

**Omega Corps HQ: Tyber's living quarters**

Tyber woke up to the sound of a doorbell, 'Why did I install that again?' Tyber thought to himself as he got out of bed and put his pants on, "Come in."

The door opened and his father was standing there, "Good morning Tyber, we need to talk."

Tyber groaned, "This early, can't it wait for a few hours?"

Robert shook his head, "No, Commander told me what you're planning on doing."

"And you're here to stop me?"

Robert shook his head, "No, in fact I'm here to help."

That took Tyber by surprise, "How do you plan on helping me get into space, and onto ARK?"

Robert motioned to the door, "Follow me."

**Omega Corps HQ: Hanger Bay 0 Dagger Squadron**

"What are you here to show me?" Tyber asked Robert, who was being cryptic about why they were there.

Robert pointed to a large jet black aircraft, "That is why we are here."

"What is that?"

Robert chuckled, "That is a prototype space fighter, the F-15X Space Eagle. That should get you to the ARK."

Tyber glanced at his father, "Wait, you're letting me fly it?"

"Yes, you are the best pilot in Omega aren't you, oh and happy birthday. It's yours"

"Birthday, what are you talking about?"

"Today's your birthday, remember?"

Tyber chuckled, "With all that's been going on I didn't even think about it." He blinked a few times, "Wait it's mine, you're giving me the plane?"

"Yeah, it'll help with most any air battle you're in, and it'll get you to the ARK and back with no problem. Besides, you'll be the best pilot for it."

Tyber chuckled, "That's true enough, and I'll take care of it."

Robert nodded, "So when are you leaving?"

Tyber shrugged, "Now I guess."

Robert started walking away but Tyber stopped him, "How does it work?"

Robert turned back, "What do you mean?"

Tyber nodded toward the Eagle, "The engines, how do they work in space."

"They use a Chaos Drive Engine, fast, efficient and capable of working in vacuum."

"Cool, thanks."

Robert nodded, "You're welcome."

**Cockpit of F-15X Space Eagle**

Tyber was amazed, he had been in multiple advanced fighters and interceptors, but none of them held a candle to this. It was so simplistic it was stupid, he could pilot this half asleep. He shook his head, 'This is advanced in design and function, but not in controls.' He put the headset on, "Space Dagger to Flight Control, requesting clearance for takeoff."

"Request granted Space Dagger, the height restrictions are canceled. Have fun Tyber."

He pushed the throttle forward, and the dual Chaos Drive Engines roared to life, pushing him toward the end of the runway at speeds that he thought were reserved for the SR-71. He pulled back on the stick and the plane shot skyward at a speed that surprised Tyber. 'Those Chaos Drives don't mess around, this speed is insane.' The Space Eagle continued to climb, passing the first levels of atmosphere with ease.

He quickly hit the top of the atmosphere, but that didn't slow him down. He just kept climbing, but there was something that surprised him further. 'How in the world am I maneuvering this good in space, there's no air for the wings to catch.' He looked behind him and saw that the engine nozzles were moving instead of the fins. 'Thrust vectoring, that would do it.'

He looked around him and he felt small against the vastness of space. In the distance he could see the ARK, the space station hadn't degraded its orbit or structurally in the sixty plus years it's been in orbit. "I'm impressed, they built it to last."

He guided the plane into the atmosphere bubble under the station and into a hanger bay. He popped the canopy and jumped out. He walked over to a computer console and hit a few buttons. "Hmm, all systems seem to be functioning normally. Surprising, I would have thought that the Black Arms attack would have rendered most of the station useless." He shrugged, "Guess I was wrong."

"You were would be right, but the repair systems did their job quite well."

Tyber spun around to be faced by an old friend, "Twilight, what are you doing up here?"

The purple hedgehog cocked his head, "I could ask you the same thing, but no matter." He smiled, "When I said I was going to go and be alone for a while, I thought this place would work."

Tyber shook his head, "That doesn't make sense, why here?"

"The entire station is completely online," Twilight explained, "And there's nobody up here."

"How long do you plan on being up here?"

Twilight shrugged, "Not sure, but probably not much longer, why?"

Tyber smiled, "Mom and Dad want to see you again, and they want you to join up with Omega Corps."

"Yeah, I miss them. But joining Omega, after what I've done, is that a good idea?"

Tyber shrugged, "Can you think of a better way to atone what you've done?"

Twilight shook his head, "Not really." He smiled, "Do I have to go through basic training?"

"No, since I did that, you know it all anyway."

Twilight chuckled, "True, I guess there is a bonus to me being flash imprinted."

Tyber nodded, "Yeah, that's the only bonus."

"Yeah, but you never told me why you came up here."

Tyber bit his lip, "Well, I felt an emotional ripple, and after investigating where it took place, it led me here."

Twilight inclined his head, "Operation Supernova, the attack on the ARK."

Tyber recoiled in the surprise, "How did you learn the name?"

"Let's just say G.U.N. never bothered to sever the information link between here and earth."

"You hacked them."

Twilight shrugged, "You say potato…"

Tyber chuckled and shook his head, "You haven't changed much have you?"

"Not really, think of me as what you would have been if you were a tactician and hacker rather than a sniper and pilot."

"Makes sense, not even a clone is identical to its template."

Twilight nodded, "Yeah, but onto more important subjects, namely, what you saw."

Tyber shrugged, "What do you want to know?"

"Namely, who you saw, what happened and what you want to do about it."

Tyber did a recap on what he saw.

Twilight nodded, "Maria, this should be interesting."


	3. Echoes of the Past

Chapter three: Echoes of the past…

**Space Colony ARK: Hanger bay 2**

Tyber got a confused look on his face, "How do you know about this?"

Twilight chuckled, "Why do you think I came here?"

Tyber shook his head, "So you picked up the ripple to?"

"Yeah, hard to miss," Twilight said while nodding, "With an energy surge that big I'm surprised I'm surprised your, I mean, our dad didn't detect it."

Tyber shrugged, "Don't know, but I think right now we need to figure out why we were called up here."

"Agreed, best place to start would be the Observation Deck, it doubled as the command level when the main one wasn't active."

Tyber glanced at him, "Wait, two things. One: how did you get up here? And two: How did you learn where to go?"

Twilight smiled, "I'm a hacker remember? And Chaos Control is definitely helpful."

**Space Colony ARK: Observation Deck**

Tyber looked around the spacious room, "Definitely big, the only thing in here is the computer."

Twilight nodded, "Yeah, didn't I say it was an observation deck?"

"Yeah you did." Tyber said while chuckling.

Twilight sighed, "You haven't changed a bit have you?"

Tyber shook his head while smiling, "Nope."

Twilight rolled his eyes and walked over to the computer, "Everything the station security cams saw is in here, along with the bios of everyone on the station."

"So is there anything on Maria Robotnik?"

Twilight shook his head, "There is, but nothing we don't already know. "

"Seriously, there's nothing new?"

Twilight started to shake his head then he smiled, "Wait here's something. It says here she had N.I.D.S., or Neuro-Immuno Deficiency Syndrome. Not sure what that is."

Tyber sighed, "I do, think someone who's had numerous doses of chemo and radiation. It nukes their Immune System, kind of. It activates itself in spurts, meaning sometimes her Immune system would work, and sometimes it wouldn't."

Twilight shook his head, "That's a lot for a twelve year old girl to go through, especially because her parents were on earth."

Tyber glanced out the window, "Yeah."

Twilight called over to him, "We're going to figure out why we're here, and what Maria has to do with it. Ok?"

Tyber smiled slightly, "Ok." He groaned and clutched his head.

"Tyber what's- ah!" Twilight groaned and clutched his head as well.

They fell to their knees and both saw a vision of the past…

**ARK: Fifty years before the events of Sonic Adventure 2**

"Maria, why was I created?"

A girl that Tyber and Twilight recognized as Maria responded, "To help people."

"That's what the Professor keeps telling me."

Maria smiled, "Hoping for a different answer?"

Shadow shrugged, "I guess, maybe just more detail on how I should help people."

Maria put a hand on his shoulder, "You've helped me."

Shadow smiled slightly, "Yeah well, that can't be helped can it?"

Maria shook her head, "No it can't."

**ARK Observation Deck: current time**

Tyber pushed himself off the floor, and saw Twilight sitting against the wall trying to catch his breath.

Twilight chuckled, "That was intense."

Tyber nodded, "More so than the previous one, by far."

Twilight groaned as he stood up slowly, "Now I'm really confused, how close were those two?"

Tyber stood up with some effort, "Don't know, but close enough for Shadow to try to blow up the planet."

Twilight shook his head, "I don't understand how anyone could be that close to someone."

Tyber glanced out the window, "What don't you get?"

Twilight shook his head, "Well, their age is an issue."

"How so, they're pretty close in age."

"He's like, not even ten at that point."

"But he's sixteen plus physically and mentally."

"Yeah I know, but still."

Tyber smiled, "Doesn't that mean you should be in love with an infant? You're only a few months old."

Twilight chuckled, "Touché, didn't think about it like that."

"Well obviously not."

Twilight laughed, "In all seriousness though, shouldn't we go and investigate the rest of the station?"

Tyber shrugged, "I guess, why we don't start with the living quarters?"

"Sounds good to me, lead the way."

**ARK living quarters: Shadow's quarters**

Tyber looked around the room, "Uh Twilight?"

Twilight who was in the adjacent room called back, "Yeah?"

"I found something."

Twilight walked into the room and chuckled, "Was he obsessed?"

Tyber shook his head, "Check the date they were printed out."

Twilight checked the date and sighed, "Great, now you've got me feeling sorry for Shadow the Hedgehog." The date was _after_ the attack, during the first ARK Crisis.

Tyber nodded, "Yeah, I think he was grasping for anything that reminded him of her." The room was covered with pictures of Maria that the security cameras had taken.

"Wouldn't you? His only friend, and potential girlfriend, was killed right in front of him."

Tyber sighed, "Yeah, I guess I would. Find anything in her room?"

Twilight shook his head, "Not really, just a bunch of stuff you would expect to find in a twelve year old girl's room."

Tyber rolled his eyes, "For us having a mission here, we're not finding much of anything."

"Agreed, maybe we'll find something in the research area."

Tyber cocked his head, "I thought G.U.N. blocked that off."

Twilight smiled, "They did, but Shadow opened it a few years ago."

"Then lead the way."

**ARK Research Area: Ultimate Life form wing**

Tyber smiled and shook his head; Twilight was in awe by all the high level computers in the room.

Twilight glanced back at Tyber, "This stuff is decades beyond what G.U.N. is using now. I mean this stuff is incredible."

Tyber chuckled, "If you say so, but aren't we supposed to be looking for clues of some kind?"

Twilight pouted, "Yeah, I guess so."

Tyber shrugged and walked over to what looked like a cloning tank. He glanced at the monitor and he saw Project Shadow. He shook his head and called out to Twilight, "Hey Twilight, this one seems, odd."

Twilight walked over to Tyber and nodded, "Yeah, it does." They walked over and they both got his by the same feeling they had in the observation deck…

**ARK Research Area: Fifty years before Sonic Adventure 2**

Shadow looked at the tank where he was 'born', "It's hard to believe that I was born in there."

Professor Gerald nodded, "Well you're the Ultimate Life Form, and did you think you had a natural birth?"

Shadow shrugged, "Not really, but more natural than that."

The Professor chuckled, "Think of it this way, all this thing did was provide nutrients for your body."

Shadow nodded, "Understood Professor."

The Professor was about to respond when Maria walked in, "Hello Grandfather, hello Shadow."

The Professor smiled warmly, "Hello Maria, how are you feeling today?"

Maria smiled and shrugged, "Great, I think this is one of the 'on' times."

He nodded, "Good." He was about to continue when his watch beeped, he glanced at Shadow, "Could you keep an eye on Maria for me, I'm apparently late for something."

Shadow smiled, "Of course Professor."

He walked out of the room.

Shadow chuckled, "Well that was easier than I thought it would be."

Maria laughed, "Yeah, who knew it would be so easy to hack his watch?"

Shadow shrugged, "Well we got him good this time didn't we?"

**ARK Research Area: current time**

Tyber woke up first and slowly stood up, using different machines to steady himself, since his balance was thrown off by the fall.

Twilight groaned and opened his eyes and sat up, "Ow, that hurt."

"Agreed, but we did learn something."

"What, that they liked to play pranks on the Professor?"

Tyber nodded, "That, and they loved each other."

**Me**: What, an Authors note? Yeah, this time I'm explaining something. The definition of what N.I.D.S. does isn't concrete. So I created my own version I guess. But how's the story so far, please leave reviews.


	4. Problems for the Present

Chapter Four: Problems for the present

**AN:** Sorry for the delay, life kept getting in the way although the writer's block didn't help.

**ARK Research Area: Ultimate Life form wing**

Twilight cocked his head, "How so?"

Tyber smirked, "He enjoyed doing that prank with her, and it looked obvious that he was attracted to her."

Twilight rubbed his chin in thought, "You know, I think you're right."

"I know I'm right, you saw what he did to avenge her."

Twilight shook his head, "I wasn't alive at the time, remember?"

"Oh right, he tried to use the ARK to destroy the Earth."

Twilight nodded, "I remember reading about that, and he used the Eclipse Cannon to blow up half the Moon. So what do we do now?"

Tyber smiled, "I think we go to the heart of the matter, to where we go to where she died."

Twilight bit his lip, "Hate to be a killjoy, but we don't know where that is."

Tyber shook his head, "Actually we do, Deck 5 Corridor 42, outside ring."

"How did you learn that?"

Tyber chuckled, "I have my ways."

**Space Colony ARK:** **Deck 5 Corridor 42, outside ring**

Tyber glanced around, "See anything?"

Twilight nodded and pointed to a corroded piece of the metal floor, "That qualify?"

Tyber nodded, "Yeah. This is what we're looking for."

Twilight cocked his head to the side, "How so, it's a piece of the floor that's damaged."

"Well, that's the same type of damage that happens when metal comes into contact with acid and not cleaned."

Twilight shook his head, "Ok, now you've lost me."

Tyber chuckled, "Blood is acidic, which is why you clean a knife after it's been in contact with blood."

Twilight inclined his head, "Oh, so this would be a blood stain if it was on carpet?"

"That's pretty much it, yeah."

Twilight nodded, "Good to know, ugh." He clutched his head and feel to the floor.

Tyber groaned and clutched his head.

**Space Colony ARK:** **Deck 5 Corridor 42, outside ring Fifty years before the events of Sonic Adventure 2**

Shadow was looking out of the viewport, watching the earth rotate underneath the station.

"Shadow, what are you doing here?"

Shadow turned around to see Maria, "Watching the earth, I've never realized just how large it is."

Maria giggled and tilted her head, "Shadow, we see it every day. It looks no bigger here than anywhere else."

Shadow shrugged, "Maybe, or maybe this is just a better view."

Maria smiled, "True, this is a better view than normal."

"And why would that be?"

Maria blushed lightly, "Uh, it just looks better here, that's all."

Shadow's eyes widened and he blushed lightly as well, "Yeah, that's what I was thinking to."

**Space Colony ARK:** **Deck 5 Corridor 42, outside ring, current day**

Tyber woke up to his head hurting more than normal, 'I must have hit it on the way down.' He thought as he stood back up.

"So, I actually woke up before you, rather than simultaneously like the other times."

Tyber glanced at Twilight, "Surprising, did you see all of it?"

Twilight nodded, "I think so, if I was right, he was thinking the same thing?"

Tyber nodded as well, "You'd be right."

"So now what, it's not as if we have anything else to learn."

Tyber shook his head, "We killed her, and I want to know why."

Twilight nodded, "Understood, but what do we know about the raid?"

Tyber shrugged, "Not much, it was classified beyond even my pay grade."

Twilight cocked his head, "Weren't able to read the file?"

Tyber shook his head again, "Yeah, but with all the black lines…"

"It was worthless, right." Twilight said as he sighed.

Tyber smirked, "It wasn't all bad; I learned that Shadow likes Swiss rolls."

Twilight gave Tyber an odd look, "Really, Swiss rolls?"

Tyber nodded, "Yes, those."

Twilight shook his head, "Now who's the one who hasn't changed?"

Tyber said while still smirking, "Shadow."

Twilight rolled his eyes, "Forget it, we've seen her death, where are the bullet holes?"

Tyber inclined his head toward part of the wall, "Over there, there should be one pistol round."

Twilight walked over and looked at the area, "Uh, Tyber. We have a problem."

Tyber groaned and stood up, "What type of problem exactly?"

"Like the bullets are wrong."

Tyber blinked, "Uh, what do you mean they're wrong."

"It's like they're bigger than a pistol round, unless they were packing bigger than the normal M9's."

Tyber walked over, "What?"

"These holes are too deep to be from a pistol, they had to have come from a rifle."

Tyber shook his head slowly, "But, a pistol killed her. That's what's on the security tape."

Twilight shrugged, "Tapes can be altered, but memories can't. We never saw what killed her."

Tyber's eyes widened, "It was an M16 no other gun sounds like it."

Twilight nodded, "So someone altered the tape, who?"

Tyber rubbed his chin, "I don't know. We need to find some more information before we take this to Command."

"In that case, I think there was a sealed chamber in the Bio-Research Center that no one could access."

Tyber smirked, "Let's go break it open."

**Bio-Research Center**

It looked like a traditional laboratory, but there were a few pods that obviously held research subject in them.

Twilight shuddered, "This place is creepy."

Tyber nodded, "Agreed, let's search this place and get out of here."

"I second that."

After a few minutes of searching, Tyber called out, "Found a DNA scanner. Like that type that's used on locks."

Twilight came over and looked at the scanner, "So that unlocks what exactly?"

Tyber shrugged, "Only one way to find out." He put his hand on the scanner and winced as the needle pierced his skin.

A few seconds later a voice echoed throughout the room, "IDENTITY CONFIRMED: DECENDENT OF SHADOW THE HEDGEHOG, UNLOCKING CLONING CHAMBER." Once it was finished speaking the door opened.

Twilight's eyes widened, "Cloning chamber?"

Tyber shrugged, "Don't know."

They entered the room and looked around; there was one cloning chamber that was smashed, and room for a second that looked as though it had been removed.

They were greeted by a hologram flashing into existence, "Greetings descendent of Shadow, I am Professor Gerald Robotnik. I have been waiting for many years for this."

Tyber and Twilight were speechless, but Twilight recovered first, "Professor, you died nearly ten years ago."

The hologram nodded, "I know."

Tyber gaped, "You know?"

The hologram smiled, "Yes, I am a semi-sentient machine, designed around Professor Gerald's nervous system and neural pathways. I have his memories, his emotions and thoughts."

Twilight nodded, "That explains a lot."

"Yes, but I assume that you two came here for a reason?"

Tyber nodded, "Yes, we are investigating the attack on the ARK. Some things aren't adding up."

The hologram rubbed its virtual chin, "You mean Operation Rising Phoenix?"

Twilight cocked his head, "Operation Rising Phoenix?" He glanced at Tyber, "I thought it was called Operation Supernova."

Tyber shrugged, "Name change?"

Gerald sighed, "Maybe, but there is something you must learn of first."

Tyber glanced at the hologram, "What is it?"

Gerald motioned to the place where the missing cloning chamber was, "In that one is a clone of Maria."

Tyber's eyes widened beyond what he thought was physically possible, "Maria!? But I thought…"

Twilight just shook his head, "Any clone that has been in development that long would be incredibly old or unstable physically."

Gerald smiled, "She isn't a normal clone. I altered some of her genetic structure, which caused her to be immune to aging."

Tyber blinked a few times, "Why would you do that?"

Gerald sighed, "I know how close Shadow was to her, so she had to be able to live as long as him."

Twilight shook his head quickly, "But, she was human. He's a hedgehog, isn't that a problem?"

Gerald smiled again, "Let's just say that I solved that problem."

Tyber nodded slowly, "Okay, so you're saying that Maria was cloned, and she's in the missing pod?"

Gerald's eyes went wide, "What do you mean she's missing?"

Twilight motioned to the empty space, "Isn't that where the pod is supposed to be?"

Gerald's virtual face fell and he nodded, "Yes, that's the pod she was supposed to be in."

Tyber smirked, "In that case, I say we find it."

Twilight raised a hand, "Later, right now we need to find out what this Operation Rising Phoenix is."

Tyber sighed, "You're right, as usual."

Gerald nodded again, "As long as you find her, take all the time you need."

Tyber bowed his head, "Thank you, we will find her."

Gerald smiled kindly at the two teenage hedgehogs, "I forgot to ask how you are related to Shadow?"

Twilight chuckled, "You tell him Tyber."

Tyber sighed, "Fine." He looked at the hologram, "We're not really related to him. I'm the son of Project Dark Star, a G.U.N. project to make a _female_ version of Shadow. They modified her long before I was born. So I have some of his DNA."

Gerald hummed, "So, you're the offspring of a G.U.N. research project?"

Tyber rubbed the back of his head, "I guess so."

Gerald nodded, "Continue."

"My father was a scientist at the time, working on the Dark Star project." Tyber continued, "He found out that she didn't know what G.U.N. was planning and voiced his concerns to the Commander, but one of scientists went ahead and altered her DNA. She nearly killed him, but my father stopped her before she did anything she'd regret. They got married a few months later. But not before they were made commanders of Omega Corps, G.U.N. Special Forces."

Gerald rubbed his chin, "So, you're not directly related to Shadow, but you seem to know about him."

Tyber nodded, "Most of the world knows about him."

Gerald inclined his head, "How do you know Shadow?"

Tyber closed his eyes, 'Here's what I was worried about.' He opened his eyes, "He works for me in Omega Corps."

Gerald smiled, "Good, then he's where he was meant to be."

Tyber's eyes widened, "What do you mean?"

Gerald chuckled, "Go research Rising Phoenix, you'll learn about it there."

Twilight shrugged, "If you say so professor."

Tyber motioned to the door, "Thanks for the info professor, but we have some things to take care of."

Gerald smiled, "Anytime, it gets lonely up here."

**ARK Hanger Bay**

Tyber sighed, "I guess this is it."

Twilight shook his head, "Not yet, I'm seeing this through till the end."

Tyber nodded once, "The fighter does sit two people…"

Tyber smirked, "Then it looks like I have a ride."

**Omega Corps Hanger Bay 0 Dagger Squadron's Hanger**

Tyber glanced around, "It feels good to be planetside."

Twilight nodded, "Agreed, now what?"

Tyber smirked, "Now we go look at Rising Phoenix."


	5. Declassified

Chapter Five: Declassified

**AN:** Hey guys, it's been awhile. *Dodges a few stray pieces of fruit*. Ok, I deserved that. Almost two months without an update, I'm sorry. I've had a severe case of writers block, and I've spent more time playing games than writing any updates. Well, the wait is over. Here's chapter five of Rising Phoenix.

**Omega Corps Data Center**

"Any luck?"

Twilight looked up from the file that he was reading, "No, every time I get close, whatever is in there I want to learn is blacked out."

Tyber sighed, "So we have nothing?"

Twilight nodded, "Yeah, Supernova is beyond even our level."

Tyber slammed his fist on the table in front of him, "Damn it!"

Twilight shook his head, "Any other time, I would say to calm down. But I agree with you, why is this thing so classified?"

Tyber shrugged, "No clue, Supernova seems to be one classified file after another." He sighed, "Have we learned anything so far?"

Twilight scoffed, "Nothing that wasn't already public knowledge, not even what firearms were used."

"Have you tried hacking it?"

"Yeah, still nothing helpful."

Tyber growled and ran his hands through his quills, "So we're at square one?"

Twilight nodded, "Yeah."

Tyber sank into a chair and frowned, "Any ideas?"

Twilight shook his head, "No, I'm not even sure if there's someone who can declassify something of this scale."

Tyber slowly broke into a smirk, "There is one person, and he owes me a favor."

Twilight cocked his head, "And who is that?"

Tyber's smirk grew, "You'll see."

**Central City: Capitol Building**

"Thank you for seeing me on such short notice Mr. President."

"Tyber, after what happened on Megalith, how can I turn down a meeting with you?"

Tyber sighed, "So you know the full story?"

The President nodded, "Yes, and what happened to Twilight. I'm still not sure to think about this Dark Form, but if you trust him, so do I."

Tyber smiled slightly, "Good to know."

The man nodded once, "So why are you here?"

"I need something declassified."

The President tilted his head, "What?"

"I need to know more about Operation Supernova, or Operation Rising Phoenix." Tyber braced himself for the answer.

"Where did you hear the second name?"

Tyber tried to look as emotionless as possible, "From a recording of Professor Gerald, it mentioned to name."

The President remained silent for a few moments and nodded, "Very well, but you may not like what you find."

Tyber smirked, "I'll be the judge of that."

The President reached into his desk, took out a flash drive and handed it to Tyber, "In that case, here."

Tyber was about to say something, but the President raised a hand to stop him, "You father told me what you were planning, I figured I would get the file ready."

**Omega Corps: Tyber's Office**

"So, any luck?" Twilight asked as he got up from the computer.

Tyber nodded, "Yeah, he gave me a flash drive with everything declassified." He tossed the flash drive to Twilight who caught it and put it in the computer.

Twilight started scanning through the files, "Huh. So the true name of the attack was Operation Rising Phoenix and, oh my God."

"What is it?"

"The goal of Rising Phoenix, it wasn't to capture Shadow."

Tyber shook his head, "But, why else would we have gone up there?"

Twilight motioned to the computer, "Read it, you won't believe me otherwise."

Tyber walked over to the computer and started reading: the first bit seemed to be useless chatter between the G.U.N. Commander and the President. But the next bit…

**From G.U.N. Commander to Professor Gerald, Your research:** Professor Gerald, it has come to my attention that you are trying to find a cure for N.I.D.S. in order to help your granddaughter. We have been attempting to create a super-soldier for a few years now. I have a proposition for you, in exchange for all the data we have on our project and considerable funding, once the cure is complete, you help us produce the super-soldier we've been looking for.

**Response from Professor Gerald:** Commander, after discussion with my colleagues, I agree to your proposal. Would it bother you, if the super-soldier and cure were one and the same?

**G.U.N. Commander:** Depends on what you mean by that professor, do you mean a serum that would cure any disease and create a super soldier? Or am I way off track?

**Professor Gerald:** Very much so Commander. I've included some of plans of Project Shadow in the transmission. See for yourself.

**G.U.N. Commander:** Amazing. This being could harness the Chaos Emeralds power, is immune to time, disease and even small arms fire. How do you plan on accomplishing this?

**Professor Gerald:** With your help. To complete him, I need energy extracted from the Chaos emeralds. A small shard of the Master Emerald would help as well.

**G.U.N. Commander:** The energy will be relatively easy, but the guardian of the Master Emerald won't be happy. But I'll get it.

Tyber glanced at Twilight, "Shadow, was a G.U.N. project?"

Twilight nodded, "Apparently so, or at least G.U.N. knew about him."

"But, didn't Shadow know about this?"

Twilight shook his head, "Doubtful, I'd be surprised if Shadow even knew that G.U.N. had knowledge of the project. Much less that they ordered his creation."

"True, but something went wrong. What was it?"

I don't know, but something turned it into an extermination mission."

Tyber cocked his head, "Any idea what?"

"Hold on." Twilight said as he continued scanning the files. A few minutes later he paled, "Phoenix, it was literal."

Tyber rubbed his temple, "Wait. What do you mean, it was literal?"

Twilight looked up at him, "I mean, they meant it was literally like a Phoenix, death, and then resurrection from the ashes."

"Twilight…"

"It was an extermination mission, but not for the scientists. The soldiers were the target."

Tyber blinked, "What."

"The targets were the soldiers." Twilight said as motioned toward the screen, "Read it yourself, what do you see."

Tyber scanned over the page, "The enlisted men, they've all been suspects in murders and other types of violent crime, but never charged due to either lack of evidence or no witnesses." He glanced at Twilight, "You mean, it was a death sentence?"

**AN: **Sorry for the lack of length, but I just need to get something out there so no one thinks I've abandoned the series or writing overall. The next chapter will be longer, and should be out in the few weeks. Unless something big happens, I will devote time to writing ok?


	6. The truth behind the Phoenix

Chapter Six: The truth behind the Phoenix

**AN:** Um, this is embarrassing. I've, been playing games and doing everything else BUT write. I'm sorry for the massive delay, it's no one's fault but my own. I hope I can put chapters out more often now, but I may get sidetracked. If I do, again, there's no one to blame but me.

**Omega Corps: Tyber's Office**

"A death sentence is an understatement; a mass execution is closer to the truth." Twilight explained.

Tyber shook his head, "What do you mean?"

"Read, the file spells out the plan G.U.N. Command came up with."

**G.U.N. Commander to Professor Gerald, Change in plans:** Professor, we have a favor to ask of you. Over the course of the last three years, numerous G.U.N. personnel have been suspected of violent of crimes, but due to lack of evidence, we haven't been able to charge them with anything.

**Response from Professor Gerald:** I'm at a loss as to what you want me to do about your problem.

**Commander:** I've heard about your ideas for the Artificial Chaos, I think they'll work quite nicely.

**Professor:** The Artificial Chaos' are prototypes, powerful yes, but prototypes. Commander, what are you planning?

**Commander:** The Chaos' have targeting systems that can be programmed to target specific targets, right?

**Professor:** That's right; I think I'm starting to see where this is going.

**Commander:** We need to have these men removed, but we're out of options.

**Professor:** Why haven't you simply discharged them?

**Commander:** Some Senator pushed through a bill that had something in the fine print that prevents us from discharging someone based on suspicion.

**Professor:** I see what you're looking for, and I can provide what you're looking for. However, I can't put the lives of everyone on the station at risk. Not unless there's something that makes the risk acceptable.

**Commander:** There might be something, you're aware of the work done by Dr. Tatchi?

**Professor:** Of course, she's one of the leading Dr.'s in the research of N.I.D.S.

**Commander:** In exchange for staging a mock attack, we'll have Dr. Tatchi transferred to the ARK. Is the acceptable?

**Professor:** Very much so Commander, I agree to your terms and I'll begin formulating a plan as soon as possible.

Tyber glanced at Twilight, "Were we wrong the entire time, was the ARK attack not an accident, but planned?"

Twilight shook his head, "Don't know, but it seems like we're missing something."

"Like what went wrong during the attack that changed it from a staged execution, into an extermination mission."

"Exactly, we need to find that out before we move forward."

Tyber closed his eyes in though, "What if, we went to the source."

Twilight cocked his head, "What do you mean, to the source?"

Tyber smirked, "There are a few of the officers that are still alive, they should know."

Twilight's eyes widened, "Survivors?"

"Yeah, only a handful of them are still alive." Tyber answered with a nod, "One of them actually lives just outside Station Square I think."

**Station Square outskirts**

"Thank you for agreeing to meet with us Captain Giles." Tyber said as he walked into the house.

The elderly man shook his head slowly, "It's my pleasure, and it hasn't been captain since I retired over twenty years ago though." He gestured toward a pair of chairs, "Please."

Twilight sat down first, "Captain, not to sound rude, but you do know why we're here correct?"

Giles nodded, "Yes, Operation Rising Phoenix. That's what anyone ever wanted to talk about for the first four years or so."

Tyber sat down and tilted his head, "Then why did you agree to meet with us?"

Giles shrugged, "I know who you two are. I figured you two are here to learn what really happened aboard the ARK. Why there are inconsistencies in the reports vs. what's up there on the station."

Tyber nodded once, "You'd be correct Captain, what can you tell us?"

Giles smiled, "Technically, nothing."

Twilight blinked once, "Explain."

Giles chuckled, "Technically, it's still classified at one of the highest levels. It would be treason to talk about it; however, what are they going to do? I'm an old man; they can't kill me, which would make it so they had to acknowledge there was a secret about the ARK that _didn't_ come out after Shadow almost destroyed the planet. They can't imprison me; I won't live through the trial."

Tyber shook his head as though trying to shake off shock, "What do you mean?"

Giles smirked, "I'm an old man, so I doubt the stress of a trial would be good for my health."

Twilight nodded, "So, what happened?"

Giles sighed, "Well….."

**G.U.N. Headquarters: Briefing room: 50 years before SA2**

"That's the plan, any questions?"

An enlisted man raised his hand, "Sir, why are we going up there anyway? They caused the problem, let them fix it."

The leader of the force shrugged, "Don't know, and I don't care. Command wants it taken care of, so we take care of it."

"It sounds like 'Command' wants us to go clean up some scientists mess, what do you want to bet that some politician has some interests that he wants protected?" A different enlisted man said with a laugh.

The commander glared at the man, "Look, I won't lie. It's probably just something a politician wants us to deal with. Regardless, we signed up to fight for G.U.N., and why renege on that now?"

The soldier scoffed, "What has G.U.N. does for us, nothing, absolutely nothing."

"Hey, G.U.N. has at least provided you guys with some of the necessities of life. Like food, clothing and housing." A lieutenant with the name 'Giles' on his nameplate said with a smirk, "Some soldiers in other countries have to provide for themselves, be happy you are this lucky."

The soldier sighed with anger obviously in the front of his mind, "Fine, you were saying colonel?"

The colonel nodded once to Giles, "The plan is to go in and take out these prototypes before they can cause any more damage than what they've already caused."

**Station Square outskirts: Present day**

"Wait that was the cover story you went with?" Tyber said incredulously.

Giles chuckled, "Kid, think about what was going on at the time. Vietnam was in its closing days, everyone in politics was in CYA (cover your ass) mode. It was the most logical choice."

Twilight nodded, "Makes sense, everyone was wary of _anything_ a politician said at the time."

Giles smirked, "Exactly, we figured if we could sell that to them we were golden." His smirk then faded, "That was, until an actual politician got involved."

Tyber cocked his head, "What do you mean?"

Giles sighed, "Well, as you two know, the only way to get at the time was though a Shuttle. Or some other form of rocket." After he got a nod from the two hedgehogs he continued, "Well, our scheduled launch date had to be moved up by a few days. Apparently, some politician made some deal with some Telecom Company and wanted to get the company's satellite in orbit as soon as he could."

Tyber's eyes widened in realization, "So the ARK..."

Giles nodded, "Had no idea we were coming." He closed his eyes, "That's when everything went to hell."


	7. When a phoenix falls

When a phoenix falls

**AN:** Hey, I was planning on having a more detailed description as to what happened during the battle, but I think that would push it into the M rated category. So I decided to cut most of it. There will be a little information, but not a lot.

Tyber's breath hitched, "From what you've said, the entire plan rode on the fact that the ARK knew you were coming. Without the knowledge that you were coming then…"

Giles nodded once, "It was going to be a bloodbath, and all that remained to be seen was who was going to provide the blood."

Twilight wiped the 'Oh my God how did that happen' look off his face, "That's, horrible."

Giles grimaced, "'Horrible' doesn't even come close as to what happened up there." He glanced at Tyber, "You've seen what happens when you take an enemy force by surprise."

Tyber's eyes widened and he had a sudden intake of breath, "Yeah, I have."

Giles nodded again, "Then you know what it was like."

Tyber simply bowed his head.

Giles sighed, "It truly was a bloodbath, there's no other way to put it."

Tyber cocked his head, "Wait, you say that like there was something hidden…"

Giles nodded, "Command was no longer interested in just having the traitors killed. They wanted them killed, and anyone on the ARK who knew what was planned erased."

**G.U.N. shuttle: 5 minutes until landing**

Giles did a final check of his Colt M-16 assault rifle and activated his helmet comm. system, "Weapons check."

After everyone on the shuttle under his command responded 'ready', he glanced at the leader of the attack who said, "The mission profile has changed, the ARK has gone renegade, unless otherwise specified, all ARK personnel are considered hostile."

Giles shifted uncomfortably in his seat, until he heard the commander say something over the command channel. "The enlisted soldier's guns are loaded with blanks; let's just hope that Professor Gerald kept up his end of the deal."

A few minutes later a voice went over the primary channel, "Prepare for landing."

When the shuttle docked, the doors opened and revealed numerous scientists who had no idea what was going on. The enlisted men automatically opened fire, somehow killing the scientists. They were the first of many to die that day.

**Station Square: current day**

Tyber blinked a few times, "Wait, I thought they had blanks, how did they kill?"

Giles sighed, "The ARK not knowing we were coming was only part of the problem."

Twilight's eyes widened in realization, "They weren't blanks, were they?"

Giles shook his head, "No, it was live ammunition. The people who were going to supply the blanks didn't have enough to fill our order, but Command didn't tell us that."

Tyber's eyes narrowed in anger, "So it wasn't just an accident, it was a cover-up."

Giles nodded, "Yes, that's a good way of putting it. Command didn't want anyone to know what happened."

Twilight closed his eyes, "Erasure, I thought that military groups doing that were a myth."

Giles shook his head, "No, it was all too real."

Tyber's eyes widened, "Wait, what happened to the Artificial Chaos? I thought that the cover story was that they were malfunctioning."

Giles nodded once, "Ah, there's the catch. Since the enlisted men were supposed to have blanks, the idea was that the scientists would play dead, and we could mop up after the Chaos security drones started tearing the enlisted forces apart."

Twilight inclined his head in realization, "So when they started firing live ammunition and the Chaos' weren't active…"

"It became clear that we had to figure it out as we went, sadly a lot of people died before we could 'complete' the mission." Giles explained, "And included in that casualty list was of course, Maria Robotnik."

Tyber sighed, "As the world learned a few years back."

"Yeah, they did." Giles said as he shook his head, "If Command hadn't sent us on that mission then she would have lived and most of this never would have happened."

Twilight shook his head, "At the risk of sounding cold, I'm kind of glad it happened."

Giles simply stared at him in confusion.

"Well, if she didn't die, then G.U.N. wouldn't have had to create their version of the Ultimate Life Form. Meaning Mary wouldn't have been changed, she wouldn't have met Robert, and Tyber wouldn't have been born."

Giles nodded, "Which by extension, means you wouldn't have existed."

Twilight smirked, "It's kind of hard to wish for your own non-existence."

Tyber chuckled, "Always the blunt one, but still that makes sense. Why would you wish for something that would remove yourself from existence?"

Twilight nodded and glanced at Giles, "Anything more we should know about Rising Phoenix?"

Giles shook his head, "No, you two know everything."

Tyber got up from his chair, "In that case, I think we're done here."

Twilight got up as well, "Thank you for your time Captain."

Giles simply smiled, "My pleasure, just use this information wisely."

Tyber nodded once and glanced at Twilight, "Let's go."

**AN:** Sorry for the lack of length, the cut battle scene cut a lot of length, and there wasn't anything more that I wanted to say. I'm a believer of not using a hundred words when ten will work. There's not much here, but there's not much more I can say that's needed for the plot. Please review. Also, I'm not accepting new OC's for the next while.


End file.
